251,806
Structures from the PDB archive

1,068,577
Computed Structure Models (CSM)

2AZR | pdb_00002azr

Crystal structure of PTP1B with Bicyclic Thiophene inhibitor

PDB DOI: https://doi.org/10.2210/pdb2AZR/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2005-09-12 Released: 2005-12-06
Deposition Author(s): Moretto, A.F., Kirincich, S.J., Xu, W.X., Smith, M.J., Wan, Z.K., Wilson, D.P., Follows, B.C., Binnun, E., Joseph-McCarthy, D., Foreman, K., Erbe, D.V., Zhang, Y.L., Tam, S.K., Tam, S.Y., Lee, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.250 (Depositor), 0.230 (DCC)
R-Value Work:
0.223 (Depositor), 0.190 (DCC)
R-Value Observed:
0.223 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Bicyclic and tricyclic thiophenes as protein tyrosine phosphatase 1B inhibitors.

Moretto, A.F., Kirincich, S.J., Xu, W.X., Smith, M.J., Wan, Z.K., Wilson, D.P., Follows, B.C., Binnun, E., Joseph-McCarthy, D., Foreman, K., Erbe, D.V., Zhang, Y.L., Tam, S.K., Tam, S.Y., Lee, J.

(2006) Bioorg Med Chem 14: 2162-2177

PubMed: 16303309 Search on PubMed
DOI: https://doi.org/10.1016/j.bmc.2005.11.005
Primary Citation Related Structures:
2AZR, 2B07

PubMed Abstract:
A novel pyridothiophene inhibitor of PTP1B was discovered by rational screening of phosphotyrosine mimics at high micromolar concentrations. The potency of this lead compound has been improved significantly by medicinal chemistry guided by X-ray crystallography and molecular modeling. Excellent consistency has been observed between structure-activity relationships and structural information from PTP1B-inhibitor complexes.

Organizational Affiliation

Chemical and Screening Science, Wyeth Research, 200 Cambridge Park Drive, Cambridge, MA 02140, USA.

Macromolecule Content

Total Structure Weight: 35.09 kDa
Atom Count: 2,658
Modeled Residue Count: 297
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase, non-receptor type 1	A	299	Homo sapiens	Mutation(s): 0 Gene Names: PTPN1, PTP1B EC: 3.1.3.48	👁 Image
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens) Explore P18031 Go to UniProtKB: P18031
PHAROS: P18031 GTEx: ENSG00000196396
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P18031
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
982 Query on 982 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	3-(CARBOXYMETHOXY)THIENO[2,3-B]PYRIDINE-2-CARBOXYLIC ACID C₁₀ H₇ N O₅ S JGZSWLHKOMFYHS-UHFFFAOYSA-N	👁 Image	Focus chain B [auth A] Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
982	BindingDB: 2AZR	Ki: 2.30e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.250 (Depositor), 0.230 (DCC)
R-Value Work: 0.223 (Depositor), 0.190 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.318	α = 90
b = 88.318	β = 90
c = 104.043	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2005-12-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-12-06
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations